In 1672 Charles II issued a Declaration of Toleration for Protestants dissenting from the Church of England; this had the effect of some dissenting meeting houses registering with the Secretary of State. The Toleration Act of 1689 enshrined the right of protestants to dissent from the Church of England and, once again, encouraged meeting houses to register voluntarily with local quarter sessions and Anglican church. Registration provided protection against persecution, laying a duty of protection upon magistrates and so was popular with nonconformists. Most registrations were made with quarter sessions until the middle of the 18th century, presumably due to the mutual antagonism of nonconformists and established Church. However, from that point registration with the Church, via the local archdeaconry began to become the favoured method, because the archdeaconry Registrar would issue a licence at any time rather than during the days each quarter when the quarter sessions met.

Visitations by the Bishop of Lincoln to Bedfordshire in the early 18th century give some idea as to the number of nonconformists in each parish from returns made by the vicar or rector. FormerCounty Archivist Patricia Bell has compiled returns from 1706 to 1720 for the Bedfordshire Historical Records Society (Volume 81, published 2002); information for Shelton includes the following:

• 1706: “[The parish] contains but 27 families in it. Of these there is never a whole family of Dissenters. Only 3 persons, in as many several families, are Independents” [often in sympathy with the Baptists]. “There is no Meeting House in the Parish. No Papists, or reputed Papists live in it”.
• 1709: “Families 25, Souls 114, of which 3 are Independents”.
• 1712: “Families 23. Of them 2 are Anabaptists [Baptists]”.
• 1717: “Families. About 22 – Eight Persons Dissenters but I cannot get information of what sect they belong to. Meeting houses None”.
• 1720: “We have six and twenty families whereof four are Dissenters which are called Independents”. “We have no Meeting-house in our Parish”.

Bedfordshire & Luton Archives & Records Service has a reasonable number of registrations of nonconformist meeting houses in both the Quarter Sessions and Archdeaconry of Bedford archives. Registration continued through the 19th century even though persecution faded away - this was because registered buildings were allowed to claim exemption from parish poor rates, were exempt from control by the Charity Commission and were allowed to be licensed to carry out marriages. These things meant that registration became almost compulsory in practice for well established nonconformist meetings. This is fortunate for the local historian because sometimes the only surviving references to a nonconformist meeting occur as registrations. One drawback with the registrations are that they do not usually inform the reader of the particular type of denomination involved, though sometimes it is possible to infer it from other evidence.

Edwin Welch researched the history of registrations in Bedfordshire for Bedfordshire Historical Records Society Volume 75 Bedfordshire Chapels and Meeting Houses [published in 1996] and found the following for Shelton:

• 17th July 1715: “The now dwelling house of Samuel Knighton [QSM 2, page134];
• 1st-8th February 1777: the house of Thomas Peck was registered by Peck himself and John Emery [ABN1/1; ABN2/43];
• 16th January 1808: the house of John Button [ABN1/1];
• 26th July-9th August 1813: the house of Henry Harris was registered by Harris himself. He may have been a Wesleyan Methodist the form is of the type and the printer used by the Methodists.

Shelton has never had a purpose built place of worship of any denomination other than the Established Church.